Ribosome 3D structures

From Proteopedia
Revision as of 11:15, 22 October 2023 by Michal Harel (talk | contribs)
Jump to navigation Jump to search

Updated on 22-October-2023 For a general description of the protein see Ribosome

    • 1ibl, 1ibm - Tt30S ribosomal subunit+THX+A-site mRNA fragment+P-site mRNA fragment+tRNA anticodon+16S rRNA
  • 30S subunit+A-site tRNA+P-site tRNA+E-site tRNA
    • 1jgo, 1jgp, 1jgq - Tt30S ribosomal subunit+P-site tRNA+A-site tRNA+E-site tRNA+tRNA Phe+mRNA +16S rRNA
  • 30S subunit + antibiotics
  • 30S subunit + ribosome recycling factor
    • 4v9d - Ec30S ribosomal subunit+16S rRNA+ribosome recycling factor + mRNA + tRNA
  • 30S subunit + elongation factor
    • 4v90 - Tt30S ribosomal subunit+THX+RNA +16S rRNA+elongation factor G
    • 6enu - Ec30S ribosomal subunit+THX+RNA +16S rRNA+elongation factor P – Cryo EM
  • 30S subunit + translation initiation factor
    • 1hr0 - Tt30S ribosomal subunit+THX+IF+16S rRNA
    • 1i96 - Tt30S ribosomal subunit+THX+IF3+16S rRNA
    • 6o7k - Ec30S ribosomal subunit+THX+IF1 + IF2 +16S rRNA - tRNA + mRNA – Cryo EM
  • 30S subunit + various proteins
    • 1x18 – TtRPS2+TtRPS7+TtRPS11+TtRPS18+GTP-binding protein ERA+RNA fragments
    • 6ny6 - Tt30S ribosomal subunit + toxin YoeB
    • 2ykr - EcRPS2 + 16S rRNA + GMPPNP + GTPase RSGA
    • 4a2i - EcRPS2 + 16S rRNA + GTPase RSGA – Cryo EM
    • 4adv - EcRPS2 + 16S rRNA + methyltransferase – Cryo EM
    • 5uz4, 5no3, 5no2 - Ec30S ribosomal subunit+ BS6 + US7 + GTPase RsgA +16S rRNA – Cryo EM
    • 6awb, 6awc, 6awd - Ec30S ribosomal subunit + RNA polymerase - Cryo EM
    • 7o5h - Ec30S + KsgA - Cryo EM
    • 6dzk - Ms30S ribosomal subunit + HPF +16S rRNA - Cryo EM
    • 6tmf - 30S ribosomal subunit + RNA-binding protein + L7AE + L41E + ATPase +16S rRNA – Thermococcus celer - Cryo EM
  • 40S ribosomal subunit
  • 40S ribosomal subunit complex
    • 6nf8, 6neq - h40S ribosomal subunit + translation initiation factor 3 - Cryo-EM
    • 5oa3 - h40S ribosomal subunit + translation initiation factor 2D - Cryo-EM
    • 6g4w - h40S ribosomal subunit + PNO1 + bystin + TSR1 + tRNA methyltransferase - Cryo-EM
    • 6g5h - h40S ribosomal subunit + RACK1 - Cryo-EM
    • 6zlw, 6zmt, 6zn5, 6zoj, 6zok, 6zol, 7k5i - h40S + SARS Nsp1 - Cryo-EM
    • 7tql - h40S ribosomal subunit + RACK1+ elF1A + eIF5B - Cryo EM
    • 5vyc - h40S ribosomal subunit + DENR-MCT-1 - Cryo-EM
    • 4kzx - r40S ribosomal subunit+ RACK1 + EIF1 – rabbit – Cryo-EM
    • 4kzy - r40S ribosomal subunit+ RACK1 + EIF1 + EIF1A – Cryo-EM
    • 4kzz - r40S ribosomal subunit+ RACK1 + EIF1A + initiator tRNA – Cryo-EM
    • 6p4g, 6p4h, 6w2s, 6w2t, 7syg, 7syh, 7syi, 7syj, 7syk, 7syl, 7sym, 7syn, 7syo, 7syp, 7syq - r40S ribosomal subunit + virus IRES – Cryo-EM
    • 7jqb - r40S + SARS Nsp1 - Cryo-EM
    • 7jqc - r40S + SARS Nsp1 + virus IRES - Cryo-EM
    • 4bts - r40S ribosomal subunit+ 18SrRNA + eIF1 + eIF1A
    • 8auv – RACK1 in 40S ribosome – tobacco - Cryo EM
    • 6fai, 6y7c - y40S ribosomal subunit + PNO1 + 20S rRNA + TSR1 + LTV1 + RIO2 - Cryo-EM
    • 6wdr - y40S ribosomal subunit + RACK1 + 20S rRNA + TSR1 - Cryo-EM
    • 6eml - y40S ribosomal subunit + PNO1 + 20S rRNA + TSR1 + LTV1 + RIO2 + essential nuclear protein 1 – Cryo-EM
    • 6rbe, 6rbd - y40S ribosomal subunit + TSR1 – Cryo-EM
    • 6zvi - y40S + Mbf1 – Cryo-EM
    • 6nd4 - y40S ribosomal subunit + SOF1 + IMP3 + MPP10 + BUD21 + NOP56 + NOP58 + NOP1 + SNU13 + RRP9 + FAF1 – Cryo-EM
    • 8cbj – y40S pre-initiation complex + Otu2 – Cryo EM
    • 4v5o - Tet40S ribosomal subunit+RACK1 – Tetrahymena thermophila
    • 5xyi - Tv40S ribosomal subunit+ RACK1 – Trichomonas vaginalis - Cryo-EM
    • 5opt – Tc40S ribosomal subunit + KSRP – Trypanosoma cruzi - Cryo-EM
    • 6okk – Pf40S ribosomal subunit + antibiotics – Plasmodium falciparum - Cryo-EM
  • 43S preinitiation
    • 6zvj, 7a09 – h43S + ABCE-1 - Cryo_EM
    • 6zon, 6zp4 – h43S + SARS Nsp1 - Cryo_EM
    • 6zce, 7a1g – y43S + ABCE-1 - Cryo_EM
    • 8cah – y43S pre-initiation complex + Otu2 – Cryo EM
    • 7ase – Tc43S + helicase - Cryo_EM
  • 48S preinitiation
    • 6fec, 6ybs, 6ybw, 6zmw, 7qp6, 7qp7 – h48S - Cryo_EM
    • 6ybd – h48S + eIF3 - Cryo_EM
    • 6yal, 6yan, 7syv – r48S + IF-3 + mRNA - Cryo_EM
    • 6yam – r48S + mRNA - Cryo_EM
    • 7syt, 7syu - r48S translation initiation complex + IRES - Cryo EM
    • 7syr, 7sys - r48S translation initiation complex + IRES + eIF2 - Cryo EM
    • 7syw, 7syx - rRACK1 in 48S translation initiation complex + IRES + eIF5B - Cryo EM
    • 6gsm, 6gsn – y48S - Cryo_EM
    • 6fyx, 6fyy – y48S + IF-5 - Cryo_EM
    • 6zu9 – y48S + ABCE-1 - Cryo_EM
    • 8cas – y48S pre-initiation complex + Otu2 – Cryo EM
  • 50S subunit
  • 50S subunit + antibiotics
  • 50S subunit + ribosome releasing factor (RRF)
    • 2rdo - Ec50S subunit +EF-G+RRF – Cryo-EM
    • 3j0d - Tt50S subunit+RRF – Cryo-EM
  • 50S subunit + various proteins
    • 2j28 - Ec50S subunit +signal recognition particle – Cryo-EM
    • 6i0y - Ec50S subunit + tRNA – Cryo-EM
    • 6s0k - Ec50S subunit + tRNA + SecA + RodZ – Cryo-EM
    • 5o2r - Ec50S subunit + antimicrobial peptide – Cryo-EM
    • 5ot7 - Ec50S subunit + EF-G – Cryo-EM
    • 6ys3 - Ec50S + peptide – Cryo-EM
    • 7bl2, 7bl3 - Ec50S + ObgE – Cryo-EM
    • 7bl6 - Ec50S+ ObgE + GMPPNP – Cryo-EM
    • 7bl4 - Ec50S + ObgE + GMPPNP + RsfS – Cryo-EM
    • 1w2b - Hm50S subunit +trigger factor N-terminal
    • 1qvf- Hm50S subunit + deacylated tRNA minihelix
    • 1q86 - Hm50S subunit +CCA-Phe-caproic acid-biotin
    • 3cma, 3cme, 1vq8, 1vq9, 1m90 - Hm50S subunit +CCA+CCA-Phe-CAP-BIO
    • 1vq4, 1vq5, 1vq7, 1vql, 1vqm, 1vqp – Hm50S subunit +transition state analog
    • 1vq6, 1vqk, 1vqn – Hm50S subunit + c-hpmn+CCA-Phe-caproic acid-biotin
    • 1vqo – Hm50S subunt + CCPMN
    • 6ppk - Bs50S subunit + ribosome biogenesis GTPase A – Cryo EM
    • 6ha8 - Bs50S subunit + VmlR – Cryo EM
    • 6htq - Bs50S subunit + RelA – Cryo EM
    • 6szs - Bs50S subunit + BrfA – Cryo EM
    • 7aqc, 7aqd, 7as8, 7as9, 7ope - Bs50S + tRNA + Rqc – Cryo EM
    • 7kgb - Mt50S + SEQ-9 – Cryo EM
  • 60S subunit
  • 60S subunit + various proteins
    • 4v6x – h60S subunit + P0 + P1 + P2 - Cryo EM
    • 4v6i – y60S subunit + P0 + P1 + P2 - Cryo EM
    • 4v8t – y60S subunit + P0 + P1 + P2 + ARX1 - Cryo EM
    • 4v7r – y60S subunit + 5S rRNA + 5.8S rRNA + 25S rRNA + P0
    • 6em5, 6em4, 6em3, 6elz, 6em1 – y60S ribosomal subunit + BRX1 + 5.8S rRNA + 25S RNA + CIC1 + ERB1 + HAS1 + MRT4 + NIP7 + ribosome biogenesis proteins + EIF-6 + nucleolar proteins – Cryo-EM
    • 6cb1, 6c0f, 5z3g – y60S ribosomal subunit + 5.8S rRNA + 25S RNA + CIC1 + HAS1 + MRT4 + NIP7 + ribosome biogenesis proteins + RNA-processing protein + nucleolar proteins + pescadillo homolog – Cryo-EM
    • 6r87, 6r84 – y60S subunit + Vms1 – Cryo EM
    • 5t6r, 5t62 – y60S subunit + Nmd3 – Cryo EM
    • 6ft6 – y60S ribosomal subunit + NOP53 – Cryo-EM
    • 6ylg, 6ylh, 6ylx, 6yly, 7bl5, 7bt6, 7btb – ypre-60S – Cryo-EM
    • 5anc, 5anb, 5an9 – sm60S subunit + P0 + SbdS + EF-Tu – slime mold - Cryo EM
    • 6qkl – sm60S subunit + P0 + SbdS + EIF-6 - Cryo EM
    • 4v6w – Dm60S subunit + P0 – Drosophila melanogaster - Cryo EM
    • 4v8p - Tet60S subunit+ 26S rRNA+ translation initiation factor 6
  • 70S ribosome
  • 70S ribosome complex with mRNA
  • 70S ribosome complex with antibiotic
  • 70S ribosome complex with release factor
    • 6eri – sRibosome + RRF + hibernation promoting factor - Cryo-EM
    • 4v5a – TtRibosome + RRF
    • 4v63, 4v7p, 6bok – TtRibosome + RF-1
    • 4v5e, 4v4r, 4v67, 4v9n – TtRibosome + RF-2
    • 4v5j – TtRibosome + RF-2 + substrate analog
    • 4v8o – TtRibosome + RF-3
    • 4v54 – EcRibosome + RRF
    • 6dnc, 6osk, 6osq – EcRibosome + RF-1 – Cryo-EM
    • 6ouo, 6og7, 6ogf, 6ogg, 6ogi, 6ot3, 6ost, 7oj0 – EcRibosome + RF-2 – Cryo-EM
    • 7o1c – EcRibosome + RF-2 + Tnac peptide – Cryo-EM
    • 5u4i, 5u9f, 5u9g – EcRibosome + RF-2 + ArfA – Cryo-EM
    • 4v89 – EcRibosome + RF-3
    • 6gxp – EcRibosome + RF-3 – Cryo EM
    • 4v85 – EcRibosome + RF-3 + mRNA + antibiotic
    • 6gwt, 6gxm, 6gxn, 6gxo – EcRibosome + RF-1+ RF-3 + P-site tRNA – Cryo-EM
  • 70S ribosome complex with various proteins
    • 4v5b – EcRibosome + PDF-binding helix
    • 4v5h – EcRibosome + Tnac leader peptide
    • 7pjs, 7pjt – EcRibosome + tRNA – Cryo EM
    • 7o1a, 7o19, 7oiz, 7p3k – EcRibosome + Tnac leader peptide – Cryo EM
    • 3j9y, 4v6v - EcRibosome+ tetracycline resistance protein + mRNA + P-tRNA – Cryo-EM
    • 6vwl, 6vwm, 6vwn – EcRibosome + HIV FSS – Cryo-EM
    • 7d6z – EcRibosome + peptide deformylase + trigger factor – Cryo-EM
    • 7d80 – EcRibosome + peptide deformylase + trigger factor + Met aminopeptidase – Cryo-EM
    • 4v6m – EcRibosome + SecYE – Cryo-EM
    • 4v4g – EcRibosome + protein Y – Cryo-EM
    • 7nww – EcRibosome + CspA – Cryo-EM
    • 7nwt – EcRibosome + virus protein – Cryo-EM
    • 6xe0, 6ztl – EcRibosome + NusG – Cryo-EM
    • 4v7i – EcRibosome +preprotein translocase – Cryo-EM
    • 4v49 - EcRibosome +general stress protein Ctc – Cryo-EM
    • 4v8g, 4v8h – TtRibosome + modulation factor
    • 4v8i - TtRibosome + ribosome-associated inhibitor
    • 4v95 – TtRibosome + YAEJ
    • 4v5k – TtRibosome + colicin E3
    • 4v7j, 4v7k – TtRibosome + toxin RelE
    • 6otr, 6oxa, 6oxi - TtRibosome + toxin YoeB
    • 6cfk – TtRibosome + His-CAM + YfiA
    • 6cfl – TtRibosome + Lys-CAM + YfiA
    • 6fkr – TtRibosome + Tur1A
    • 7jql, 7jqm – TtRibosome + mRNA + tRNA + antimicrobial peptide
    • 5zlu – TtRibosome + ABC-F – Cryo-EM
    • 6dzi – MsRibosome + MPY – Cryo-EM
    • 7msc, 7msh, 7msm, 7msz – MtRibosome + Etta – Cryo-EM
    • 7nhn – Ribosome + ABCF – Listeria monocytogenes – Cryo-EM
    • 6v39, 6v3a – AbRibosome + tRNA – Cryo EM
    • 7p7u - EfRibosome + P-tRNA - Cryo-EM
    • 7nhk – EfRibosome + LsaA – Cryo EM
    • 7p7q, 7p7s, 7p7t – EfRibosome + ABCF – Cryo-EM
  • 70S ribosome complex with tRNA mRNA
    • 6gsj, 6gsk, 6gsl – TtRibosome + A-site tRNA-Thr + mRNA + tRNA-fMet
    • 6n1d – TtRibosome + mRNA + tRNA
    • 6bz7, 6bz8 – TtRibosome + A-site tRNA-Leu
    • 5vpo, 5vpp, 6ndk – TtRibosome + tRNA-SufA6
    • 6n9e, 6n9f – TtRibosome + mRNA + P-site tRNA
    • 6uo1 – TtRibosome + mRNA + A-site tRNA + P-site tRNA + E-site tRNA
    • 6q95, 6q97 – TtRibosome + A-site tRNA – Cryo-EM
    • 6q98 – TtRibosome + P-site tRNA – Cryo-EM
    • 6q9a – TtRibosome + E-site tRNA – Cryo-EM
    • 5uq7 – TtRibosome + A-site tRNA + dnaX – Cryo-EM
    • 5uq8 – TtRibosome + E-site tRNA + dnaX – Cryo-EM
    • 6cfj – TtRibosome + His-CAM + A-site tRNA + P-site tRA + E-site tRNA + mRNA + antibiotic
    • 7mt2, 7mt3, 7mt7 – MtRibosome + P-tRNA + E-tRNA – Cryo-EM
    • 7pju – EcRibosome + A-tRNA + P-tRNA + E-tRNA – Cryo-EM
  • 70S ribosome complex with elongation factor
  • 80S ribosome
  • 80S ribosome complexes
    • 6r6p – hRibosome + XBP1u - Cryo-EM
    • 6zvh – hRibosome + EDF1 - Cryo-EM
    • 6z6n – hRibosome + EBP1 - Cryo-EM
    • 6z6m – hRibosome + EBP1 +EF-2 + SERBP1 - Cryo-EM
    • 6z6l – hRibosome + CCDC124 - Cryo-EM
    • 6zm7 – hRibosome + CCDC124 + EBP1 - Cryo-EM
    • 6z6e – hRibosome + CCDC124 + SARS Nsp1 - Cryo-EM
    • 6zmi – hRibosome + SARS Nsp1 - Cryo-EM
    • 6zmo – hRibosome + EF-1 + SARS Nsp1 - Cryo-EM
    • 6olg, 6oli – hRibosome + drug - Cryo-EM
    • 6olz, 6xa1 – hRibosome + tRNA + drug - Cryo-EM
    • 6ole, 6olf, 6om0, 6om7 – hRibosome + A-site tRNA + P-site tRNA + drug - Cryo-EM
    • 7nfx – hRibosome + SRP + SRP receptor - Cryo-EM
    • 8g61 - hRribosome + mRNA - Cryo EM
    • 6fti, 6ftj - dRibosome + oligosaccharyltransferase + Sec61 - Cryo-EM
    • 6ftg - dRibosome + OST - Cryo-EM
    • 3j0l, 3j0o, 3j0p, 3j0q - rRibosome+ mRNA – Cryo-EM
    • 6mte, 6mtd – rRibosome + EF2 + SERBP1 - Cryo-EM
    • 6d9j, 6d90 – rRibosome + RF-1 + P-site tRNA - Cryo-EM
    • 7o80 – rRibosome + RF-1 +ABCE-1 - Cryo-EM
    • 7nwg – rRibosome + A-tRNA + P-site tRNA + E-tRNA + antibiotic- Cryo-EM
    • 6frk – rRibosome + SRP + SRP receptor - Cryo-EM
    • 6hcj – rRibosome + A-site tRNA + P-site tRNA - Cryo-EM
    • 6mtb – rRibosome + P-site tRNA + Z-site tRNA - Cryo-EM
    • 6mtc – rRibosome + Z-site tRNA + IFRD2 - Cryo-EM
    • 6r5q – rRibosome + XBP1u - Cryo-EM
    • 6r6g – rRibosome + XBP1u + SRP - Cryo-EM
    • 6r7q – rRibosome + XBP1u + Sec61 - Cryo-EM
    • 6t59 – rRibosome +b-tubulin- Cryo-EM
    • 6z6j, 6z6k – rRibosome + Lso2 - Cryo-EM
    • 7nwh, 7nwi – rRibosome + antibiotic – Cryo EM
    • 6p5i, 6p5j, 6p5k, 6p5n, 6ip6, 6ip8, 6zvk, 7a01 - rRibosome + IRES – Cryo-EM
    • 4v6w - DmRibosome + EF2 + guanine nucleotide-binding protein – Cryo-EM
    • 7ls1, 7ls2 – mRibosome + EF2 - Cryo-EM
    • 7osa, 7osm – yRibosome + EF2 + GTP
    • 4v4b – yRibosome + EF2 + antifungal - Cryo-EM
    • 6gqv, 6gqb, 6gq1 – yRibosome + EF2 + mRNA + tRNA - Cryo-EM
    • 5tga, 5tgm – yRibosome + A-site tRNA-Pro
    • 5tbw, 5obm, 5on6 – yRibosome + antibiotic
    • 7azy – yRibosome + antibiotic – Cryo EM
    • 6hd7 – yRibosome + NatA – Cryo EM
    • 6s47 – yRibosome + New1 – Cryo EM
    • 6hhq – yRibosome + C45 – Cryo EM
    • 6q8y – yRibosome + Xrn1 – Cryo EM
    • 7rr5 – yRibosome + Rbg1 + Tma46 – Cryo EM
    • 6xir – yRibosome + ubiquitin – Cryo EM
    • 7of1, 7oh3, 7ohq, 7ohp, 7ohr, 7ohs, 7oht, 7ohu, 7ohv, 7ohw, 7ohx, 7ohy – yRibosome + Nog1-TAP – Cryo EM
    • 6woo – yRibosome + tRNA-Met + eIF5B + GDP – Cryo EM
    • 7b7d – yRibosome + A-tRNA + P-tRNA + EF3 – Cryo EM
    • 7nrc, 7nrd – yRibosome + Gcn1 + A-tRNA + P-tRNA + eIF5A + Rbg2 + Gir2 – Cryo EM
    • 8evp, 8evs, 8evt, 8ewc – y80S ribosome + IRES – Cryo EM
    • 8bqd, 8bqx – y80S ribosome + Map1 – Cryo EM
    • 7mpi, 7mpj – y80S ribosome + Stm1 – Cryo EM
    • 7zw0 – y80S ribosome + FAP – Cryo EM
    • 7zpq, 7zrs, 7zuw – y80S ribosome + RQT – Cryo EM
    • 8cdr, 8ceh, 8cf5, 8civ, 8cku, 8cmj – y80S ribosome + eEF2 – Cryo EM
    • 8eub, 8evq, 8evr, 8ewb – y80S ribosome + IRES + eEF2 + GDP – Cryo EM
    • 6zu5 – Ribosome + Lso2 – Paranosema locustae - Cryo-EM
    • 4v7h - TlRibosome+P-site tRNA – Thermomyces lanuginosus
    • 5umd – PfRibosome + mefloquin - Cryo-EM
    • 5osg – LdRibosome + KSRP - Cryo-EM
    • 6uz7 – Ribosome + E-site tRNA + P-site tRNA + IF5B – Kluyveromyces lactis - Cryo-EM
  • 90S pre-ribosome
  • 100S ribosome
  • Mitoribosome or mitochondrial ribosome
  • 28S small subunit
    • 6gaz – p28S ribosomal subunit – pig - Cryo-EM
    • 3jd5 – b28S ribosomal subunit - Cryo-EM
    • 6sg9, 6sga, 6sgb – Tb28S ribosomal subunit - Cryo-EM
    • 6hiy, 6hiw – Tb28S ribosomal subunit+ IF-3 - Cryo-EM
    • 6yw5 – Nc28S - Cryo-EM
  • 39S large subunit
  • 55S small+large mitoribosome

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Jaime Prilusky, Alexander Berchansky, Wayne Decatur, Michal Harel, Joel L. Sussman
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=Ribosome_3D_structures&oldid=3918676"